I'm not sure where you got the mssql08.properties file from, but you can try stripping it down to just description, connectionSpec (and associated referenced variable descriptions) and driver. You won't get all of the details that are available, but it should help track down what's going wrong.

I think I've gone about this the wrong way…..
Please disregard the reference to mssql08.properties … it's just used
I basically have a MSSQL 2008 Spatial server and I'd like to use Schemaspy to produce a diagram.

My SQL DB is <server>\&lt;instance>\&lt;database>

I've googled for some information and found something about using the jTDS driver instead when the "The "variant" data type is not supported." error is found.

The latest beta version (http://schemaspy.sourceforge.net/schemaSpy.jar) has two .properties files for jTDS. mssql-jtds requires host, port and db while mssql-jtds-instance also requires an instance to be specified. They are otherwise logically identical via inheritance. It looks like you'd want to use mssql-jtds-instance in your scenario and specify your instance with -instance instanceName.

I'm confused as to why you didn't see dots as it progressed. There's typically (approx) one per table as it collects the metadata details, then one per summary generated, and finally one per table as it generates the graphs.

I assume the resultant overview graphs would be mostly unreadable with that many tables. Assuming, of course, that Graphviz didn't choke while attempting to generate them.